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Clone History Shapes Populus Drought Responses

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ABSTRACT: Just as animal monozygotic twins can experience different environmental conditions by being reared apart, individual genetically-identical trees of the genus Populus can also be exposed to contrasting environmental conditions by being grown in different locations. As such, clonally-propagated Populus trees provide an opportunity to interrogate the impact of individual environmental history on current response to environmental stimuli. To test the hypothesis that current responses to an environmental stimulus, drought, are contingent on environmental history, the transcriptome-level drought responses of three economically important hybrid genotypes: DN34 (Populus deltoides x P. nigra); Walker (P. deltoides var. occidentalis x (P. laurifolia x P. nigra)); and, Okanese (‘Walker’ x (P. laurifolia x P. nigra)) derived from two different locations were compared. Strikingly, differences in transcript abundance patterns in response to drought were based on differences in geographic origin of clones for two of the three genotypes. This observation was most pronounced for the genotypes with the longest time since establishment and last common propagation. Differences in genome-wide DNA methylation paralleled the transcriptome level trends, where the clones with the most divergent transcriptomes and clone history had the most marked differences in the extent of total DNA methylation, suggesting an epigenetic basis for the clone-history-dependent transcriptome divergence. The data provide insights into the interplay between genotype and environment in the ecologically and economically important Populus genus, with implications for both the industrial application of Populus trees, and the evolution and persistence of these important tree species. 72 arrays total. 2 time points. 2 water regimes. 3 biological replicates per treatment

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Project description:Just as animal monozygotic twins can experience different environmental conditions by being reared apart, individual genetically-identical trees of the genus Populus can also be exposed to contrasting environmental conditions by being grown in different locations. As such, clonally-propagated Populus trees provide an opportunity to interrogate the impact of individual environmental history on current response to environmental stimuli. To test the hypothesis that current responses to an environmental stimulus, drought, are contingent on environmental history, the transcriptome-level drought responses of three economically important hybrid genotypes: DN34 (Populus deltoides x P. nigra); Walker (P. deltoides var. occidentalis x (P. laurifolia x P. nigra)); and, Okanese (‘Walker’ x (P. laurifolia x P. nigra)) derived from two different locations were compared. Strikingly, differences in transcript abundance patterns in response to drought were based on differences in geographic origin of clones for two of the three genotypes. This observation was most pronounced for the genotypes with the longest time since establishment and last common propagation. Differences in genome-wide DNA methylation paralleled the transcriptome level trends, where the clones with the most divergent transcriptomes and clone history had the most marked differences in the extent of total DNA methylation, suggesting an epigenetic basis for the clone-history-dependent transcriptome divergence. The data provide insights into the interplay between genotype and environment in the ecologically and economically important Populus genus, with implications for both the industrial application of Populus trees, and the evolution and persistence of these important tree species. Overall design: 72 arrays total. 2 time points. 2 water regimes. 3 biological replicates per treatment

Project description:As exposure to episodic drought can impinge significantly on forest health and the establishment of productive tree plantations, there is great interest in understanding the mechanisms of drought response in trees. The ecologically dominant and economically important genus Populus, with its sequenced genome, provides an ideal opportunity to examine transcriptome level changes in trees in response to a drought stimulus. The transcriptome level drought response of two commercially important hybrid Populus clones (P. deltoides · P. nigra, DN34, and P. nigra · P. maximowiczii, NM6) was characterized over a diurnal period using a 4 · 2 · 2 completely randomized factorial ANOVA experimental design (four time points, two genotypes, and two treatment conditions) using Affymetrix Poplar GeneChip microarrays. Notably, the specific genes that exhibited changes in transcript abundance in response to drought differed between the genotypes and/or the time of day that they exhibited their greatest differences. This study emphasizes the fact that it is not possible to draw simple, generalized conclusions about the drought response of the genus Populus on the basis of one species, nor on the basis of results collected at a single time point. The data derived from our studies provide insights into the variety of genetic mechanisms underpinning the Populus drought response, and provide candidates for future experiments aimed at understanding this response across this economically and ecologically important genus. Overall design: 48 arrays total. 2 genotypes (DN34, NM6), 4 time points (midnight, pre-dawn, mid-day, late day), 2 water regimes (well-watered, water-limited). 3 biological replicates per treatment.

Project description:As exposure to episodic drought can impinge significantly on forest health and the establishment of productive tree plantations, there is great interest in understanding the mechanisms of drought response in trees. The ecologically dominant and economically important genus Populus, with its sequenced genome, provides an ideal opportunity to examine transcriptome level changes in trees in response to a drought stimulus. The transcriptome level drought response of two commercially important hybrid Populus clones (P. deltoides · P. nigra, DN34, and P. nigra · P. maximowiczii, NM6) was characterized over a diurnal period using a 4 · 2 · 2 completely randomized factorial ANOVA experimental design (four time points, two genotypes, and two treatment conditions) using Affymetrix Poplar GeneChip microarrays. Notably, the specific genes that exhibited changes in transcript abundance in response to drought differed between the genotypes and/or the time of day that they exhibited their greatest differences. This study emphasizes the fact that it is not possible to draw simple, generalized conclusions about the drought response of the genus Populus on the basis of one species, nor on the basis of results collected at a single time point. The data derived from our studies provide insights into the variety of genetic mechanisms underpinning the Populus drought response, and provide candidates for future experiments aimed at understanding this response across this economically and ecologically important genus. 48 arrays total. 2 genotypes (DN34, NM6), 4 time points (midnight, pre-dawn, mid-day, late day), 2 water regimes (well-watered, water-limited). 3 biological replicates per treatment.

Project description:In a context of climate changes, water availability is expected to become a limiting factor for plant growth and to have an impact on forest health. In order to identify genes involved in shoot phenotypic plasticity in response to variations in water availability in trees, gene expression patterns were investigated in the shoot apical meristem (SAM) of Populus deltoides × P. nigra hybrid cuttings submitted to a moderate water deficit followed by a rewatering step. Methylome response was also studied and is another GEO submission. Several gene clusters with expression patterns specific to SAM drought response as well as specific to the rewatering condition could be identified. Among them, genes involved in phytohormone pathways like brassinosteroids were found. Overall design: Populus deltoides × P. nigra 'Carpaccio' hybrid cuttings were submitted to 3 water conditions: non-limiting, water deficit and water deficit/rewatering cycle (14 days treatment). At the end of the experiment, buds were collected and SAM maually isolated for 6 individuals per condition. Total RNA were independently extracted from 3 individuals per condition and used for microarray analyses.

Project description:In a context of climate changes, water availability is expected to become a limiting factor for plant growth and to have an impact on forest health. In order to identify genes involved in shoot phenotypic plasticity in response to variations in water availability in trees, gene expression patterns were investigated in the shoot apical meristem (SAM) of Populus deltoides × P. nigra hybrid cuttings submitted to a moderate water deficit followed by a rewatering step. Methylome response was also studied and is another GEO submission. Several gene clusters with expression patterns specific to SAM drought response as well as specific to the rewatering condition could be identified. Among them, genes involved in phytohormone pathways like brassinosteroids were found. Populus deltoides × P. nigra 'Carpaccio' hybrid cuttings were submitted to 3 water conditions: non-limiting, water deficit and water deficit/rewatering cycle (14 days treatment). At the end of the experiment, buds were collected and SAM maually isolated for 6 individuals per condition. Total RNA were independently extracted from 3 individuals per condition and used for microarray analyses.

Project description:Drought is a major limitation to the growth and productivity of trees in the ecologically and economically important genus Populus. The ability of Populus trees to contend with drought is a function of the responsiveness of their genome to this environmental insult, involving reconfiguration of the transcriptome to appropriately remodel growth, development and metabolism. The Populus drought transcriptome is shaped by interspecific genotypic variation, but the extent to which intraspecific variation shapes the drought transcriptome has not yet been examined. Here we test hypotheses aimed at examining the extent of intraspecific variation in the drought transcriptome. Transcriptome remodeling in response to water-deficit conditions was examined in six different Populus balsamifera L. genotypes using Affymetrix GeneChip technology. There were significant differences in the transcriptomes of the genotypes in response to water-deficit conditions; however, a common species-level response could also be identified across all individuals. Genotypes that had more similar drought-responsive transcriptomes also had fewer genotypic differences, as determined by microarray-derived single feature polymorphism (SFP) analysis, suggesting that responses may be conserved across individuals that share a greater degree of genotypic similarity. This work highlights the fact that a core species-level response can be defined; however, the underpinning genotype-derived complexities of the drought response in Populus must be taken into consideration when defining both species- and genus-level responses. Overall design: 72 arrays total. 6 genotypes, 2 time points. 2 water regimes. 3 biological replicates per treatment

Project description:Drought is a major limitation to the growth and productivity of trees in the ecologically and economically important genus Populus. The ability of Populus trees to contend with drought is a function of the responsiveness of their genome to this environmental insult, involving reconfiguration of the transcriptome to appropriately remodel growth, development and metabolism. The Populus drought transcriptome is shaped by interspecific genotypic variation, but the extent to which intraspecific variation shapes the drought transcriptome has not yet been examined. Here we test hypotheses aimed at examining the extent of intraspecific variation in the drought transcriptome. Transcriptome remodeling in response to water-deficit conditions was examined in six different Populus balsamifera L. genotypes using Affymetrix GeneChip technology. There were significant differences in the transcriptomes of the genotypes in response to water-deficit conditions; however, a common species-level response could also be identified across all individuals. Genotypes that had more similar drought-responsive transcriptomes also had fewer genotypic differences, as determined by microarray-derived single feature polymorphism (SFP) analysis, suggesting that responses may be conserved across individuals that share a greater degree of genotypic similarity. This work highlights the fact that a core species-level response can be defined; however, the underpinning genotype-derived complexities of the drought response in Populus must be taken into consideration when defining both species- and genus-level responses. 72 arrays total. 6 genotypes, 2 time points. 2 water regimes. 3 biological replicates per treatment

Project description:A microarray analysis of whole-genome gene expression and single feature polymorphism in a (Populus trichocarpa X Populus deltoides) X Populus deltoides pseudo-backcross pedigree. Genetic variation in gene expression was quantified for 55,793 predicted gene models based on a single probe per gene. Concurrently, sequence-level polymorphism was analyzed based on dedicated probes identified in a pilot study comprised of the two parent genotypes (GPL7169). Resultant data contributed to a high density genetic map and to analysis of the genetic architecture of gene expression in Populus. Keywords: Genetic analysis of gene expression and polymorphism, eQTL Data include one biological replicate of 178 segregating pseudobackcross progeny analyzed for gene expression (GE) using one probe per gene for 55793 independent gene models (probes E_POPLARSxxxxxPxxxxx) and single feature sequence polymorphism (SFP) using one probe per gene for 12084 independent gene models (probes G_POPLARSxxxxxPxxxxx). GE and SFP probes were selected from 6-7 probes per gene previously tested in a pilot study of the two parent trees of the cross (Populus deltoides X Populus trichocarpa).

Project description:In a context of climate changes, water availability is expected to become a limiting factor for plant growth and to have an impact on forest health. In order to identify genes involved in shoot phenotypic plasticity in response to variations in water availability in trees, DNA methylation patterns were investigated in the shoot apical meristem (SAM) of Populus deltoides × P. nigra hybrid cuttings submitted to a moderate water deficit followed by a rewatering step. Transcriptomic response was also studied and is another GEO submission. Populus deltoides × P. nigra 'Carpaccio' hybrid cuttings were submitted to 3 water conditions: non-limiting, water deficit and water deficit/rewatering cycle (14 days treatment). At the end of the experiment, buds were collected and SAM maually isolated for 6 individuals per condition. DNA was extracted from 3 individuals per condition and pooled. For each condition, methylated DNA was isolated using a MethylDNA Immunoprecipitation (MeDIP) and both total DNA and MeDIP fraction were hybridised to microarrays.

Project description:A microarray analysis of whole-genome gene expression and single feature polymorphism in a (Populus trichocarpa X Populus deltoides) X Populus deltoides pseudo-backcross pedigree. Genetic variation in gene expression was quantified for 55,793 predicted gene models based on a single probe per gene. Concurrently, sequence-level polymorphism was analyzed based on dedicated probes identified in a pilot study comprised of the two parent genotypes (GPL7169). Resultant data contributed to a high density genetic map and to analysis of the genetic architecture of gene expression in Populus. Keywords: Genetic analysis of gene expression and polymorphism, eQTL Overall design: Data include one biological replicate of 178 segregating pseudobackcross progeny analyzed for gene expression (GE) using one probe per gene for 55793 independent gene models (probes E_POPLARSxxxxxPxxxxx) and single feature sequence polymorphism (SFP) using one probe per gene for 12084 independent gene models (probes G_POPLARSxxxxxPxxxxx). GE and SFP probes were selected from 6-7 probes per gene previously tested in a pilot study of the two parent trees of the cross (Populus deltoides X Populus trichocarpa).